Alignment of IL_84476.1 sequences from 3D to the JAR3D model

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The correspondence between sequences from 3D structures and the motif group is shown in blue and the JAR3D alignment of the sequences to the motif group is shown in black. Occasionally the two disagree, in which case the JAR3D alignment is shown in red.
Column number:
Node in JAR3D model:
Insertion positions indicated by I:
Position in motif group:		1
1
I

2
2

1
3
2
I

4
3

2
5
3
I

6
4


7
3
I

8
3

3
9
2
I

10
2

4
11
1
I


In
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IL_84476.1_Instance_1 IL_84476.1,IL_8P9A_363,C3349_G3356CCGUUG
IL_84476.1_Sequence_1 IL_84476.18P9A_C_3349_G_3356CC*GUUGtrue100000.00
IL_84476.1_Instance_2 IL_84476.1,IL_8CRE_142,C3314_G3321CCGUUG
IL_84476.1_Sequence_2 IL_84476.18CRE_C_3314_G_3321CC*GUUGtrue100000.00
IL_84476.1_Instance_3 IL_84476.1,IL_8ZAU_001,C11_G41CGCUAG
IL_84476.1_Sequence_3 IL_84476.18ZAU_C11_G41CG*CUAGtrue85001.43
IL_84476.1_Instance_4 IL_84476.1,IL_7D3J_001,C11_G19CCGUUG
IL_84476.1_Sequence_4 IL_84476.17D3J_C11_G19CC*GUUGtrue100000.00
IL_84476.1_Instance_5 IL_84476.1,IL_7Q80_001,C13_G38CGCUAG
IL_84476.1_Sequence_5 IL_84476.17Q80_C13_G38CG*CUAGtrue85001.43
IL_84476.1_Instance_6 IL_84476.1,IL_7EU9_001,C11_G19CCGUUG
IL_84476.1_Sequence_6 IL_84476.17EU9_C11_G19CC*GUUGtrue100000.00
IL_84476.1_Instance_7 IL_84476.1,IL_7Q80_003,C35_G14CUAGCG
IL_84476.1_Sequence_7 IL_84476.17Q80_C35_G14CUAG*CGtrue64003.44
IL_84476.1_Instance_8 IL_84476.1,IL_1R3E_002,G408_C416GUUCGCC
IL_84476.1_Sequence_8 IL_84476.11R3E_G408_C416GUUCG*CCtrue53004.51
IL_84476.1_Instance_9 IL_84476.1,IL_1R3E_001,G408_C416GUUCGCC
IL_84476.1_Sequence_9 IL_84476.11R3E_G408_C416GUUCG*CCtrue53004.51
IL_84476.1_Instance_10 IL_84476.1,IL_3R2D_001,G2_C11GCUCGC
IL_84476.1_Sequence_10 IL_84476.13R2D_G2_C11GCUC*GCtrue66003.26
IL_84476.1_Instance_11 IL_84476.1,IL_6JXM_001,A34_U56ACGAUU
IL_84476.1_Sequence_11 IL_84476.16JXM_A34_U56AC*GAUUtrue82001.69
IL_84476.1_Instance_12 IL_84476.1,IL_6LTU_001,C11_G19CUAUUG
IL_84476.1_Sequence_12 IL_84476.16LTU_C11_G19CU*AUUGtrue97000.27
IL_84476.1_Instance_13 IL_84476.1,IL_4ERD_001,C120_G147CGACGG
IL_84476.1_Sequence_13 IL_84476.14ERD_C120_G147CGAC*GGtrue49004.83

Conserved interactions between motif group positions in IL_84476.1:
1 2 s35 
1 4 cWW 
2 3 cWW 
2 4 s55 
3 4 s35
JAR3D SCFG/MRF model for IL_84476.1:
Character Definition | A,C,G,U,* // Identity and order of characters in matrices
InitialNode  | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [1] | Right Index [4] // Initial node
BasepairNode | Deletion Probability [0.0000000002643351] | Pair Probability [[0.008631686,0.016437923,0.009848509,0.189184836,0.000000000],[0.017448891,0.008723077,0.266011264,0.012104366,0.000000000],[0.009898469,0.210629286,0.001882854,0.023934598,0.000000000],[0.180847211,0.011941002,0.023214651,0.009261378,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.612007709,0.003236579,0.230209054,0.153884631,0.000632604,0.000029423] | Left Letter Distribution [0.178571429,0.250000000,0.107142857,0.464285714,0.000000000] | Right Length Distribution [0.382167478,0.003821675,0.611541458,0.002351800,0.000117590] | Right Letter Distribution [0.194444444,0.027777778,0.027777778,0.750000000,0.000000000] | Left Index [1] | Right Index [4] // Basepair C3349 - G3356 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.008641799,0.016568117,0.009864960,0.180145637,0.000000000],[0.017321684,0.008717222,0.247681545,0.012081646,0.000000000],[0.009883410,0.228987209,0.001883003,0.022298134,0.000000000],[0.189915970,0.011965123,0.024857566,0.009186974,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [3] // Basepair C3350 - G3353 cWW 
HairpinNode  | Num Bases [1] | Left Index [3] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node type *
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,1.000000000]] // Hairpin for truncation
Sequences of instances from IL_84476.1:
> IL_84476.1  8P9A C 3349 G 3356
CC*GUUG
> IL_84476.1  8CRE C 3314 G 3321
CC*GUUG
> IL_84476.1  8ZAU C   11 G   41
CG*CUAG
> IL_84476.1  7D3J C   11 G   19
CC*GUUG
> IL_84476.1  7Q80 C   13 G   38
CG*CUAG
> IL_84476.1  7EU9 C   11 G   19
CC*GUUG
> IL_84476.1  7Q80 C   35 G   14
CUAG*CG
> IL_84476.1  1R3E G  408 C  416
GUUCG*CC
> IL_84476.1  1R3E G  408 C  416
GUUCG*CC
> IL_84476.1  3R2D G    2 C   11
GCUC*GC
> IL_84476.1  6JXM A   34 U   56
AC*GAUU
> IL_84476.1  6LTU C   11 G   19
CU*AUUG
> IL_84476.1  4ERD C  120 G  147
CGAC*GG